Description

Statistical Analysis for Genetic Epidemiology (S.A.G.E.) is a collection of compiled C++ programs that perform a wide variety of genetic analyses. The range of functionality includes tools for:

• extracting summary statistics describing the data and evaluating general data quality
• estimating allele frequencies
• estimating heritability and familial correlations
• inferring mixture models for genetic transmission, and penetrance functions, including variable age of onset
• estimating identity-by-descent (IBD) allele sharing probabilities between relative pairs
• performing model-based linkage analysis
• performing model-free linkage analysis
• performing transmission/disequilibrium (TDT) analysis
• analyzing trait/allele associations

The programs of SAGE are intended to be used on the Helix platform of the Helix Systems. They are under /usr/local/sage/bin . To start the program, type the full path of the program followed by required parameters. SAGE programs include:

• assoc
• ageon
• decipher
• fcor
• freq
• genibd
• lodpal
• lodlink
• markerinfo
• mlod
• pedinfo
• reltest
• segreg
• sibpal
• tdtex

Version

Type /usr/local/sage/bin/pedinfo on command line

Sample session

Sage example files can be copied from /usr/local/sage/Examples.

% /usr/local/sage/bin/pedinfo InputFile.parameters InputFile.Pedigree

PEDINFO -- 1 Aug 2006 14:04:05 -- [S.A.G.E. v5.1.1; 12 Dec 2005]
COPYRIGHT (C) 2005 CASE WESTERN RESERVE UNIVERSITY

Reading Parameter File....................done.
Reading Pedigree File.....................
from InputFile.parameters...........done.
Sorting Pedigrees.........................done.
Generating statistics.....................done.

Analysis complete!

Add to your path /usr/local/sage/bin if run sage programs a lot. This directory contains all executables in the package.

For csh or tcsh users, issue this command: % set path=( /usr/local/eigensoft/bin ${path} )
For bash/ksh/sh users, issue this command: % PATH=/usr/local/eigensoft/bin:$PATH

Documentation

sage_UserDoc.pdf